{
  "_id": "69e1fa01c5259ad4cd941e1e",
  "Package": "canaper",
  "Title": "Categorical Analysis of Neo- And Paleo-Endemism",
  "Version": "1.0.1.9000",
  "Authors@R": "c(\nperson(given = \"Joel H.\",\nfamily = \"Nitta\",\nrole = c(\"aut\", \"cre\"),\nemail = \"joelnitta@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4719-7472\")),\nperson(given = \"Shawn W.\",\nfamily = \"Laffan\",\nrole = c(\"ctb\", \"dtc\")),\nperson(given = \"Brent D.\",\nfamily = \"Mishler\",\nrole = c(\"ctb\", \"dtc\")),\nperson(given = \"Wataru\",\nfamily = \"Iwasaki\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-9169-9245\")),\nperson(given = \"Klaus\",\nfamily = \"Schliep\",\nrole = c(\"rev\"),\ncomment = c(ORCID = \"0000-0003-2941-0161\"))\n)",
  "Description": "Provides functions to analyze the spatial distribution of\nbiodiversity, in particular categorical analysis of neo- and\npaleo-endemism (CANAPE) as described in Mishler et al (2014)\n<doi:10.1038/ncomms5473>. 'canaper' conducts statistical tests\nto determine the types of endemism that occur in a study area\nwhile accounting for the evolutionary relationships of species.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE, roclets = c (\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\", \"srr::srr_stats_roclet\"))",
  "RoxygenNote": "7.2.3",
  "URL": "https://github.com/ropensci/canaper,\nhttps://docs.ropensci.org/canaper/",
  "BugReports": "https://github.com/ropensci/canaper/issues",
  "Language": "en-US",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libgmp3-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2023-05-07 05:24:45 UTC",
  "RemoteUrl": "https://github.com/ropensci/canaper",
  "RemoteRef": "main",
  "RemoteSha": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-04-17 09:05:23 UTC",
    "User": "root"
  },
  "Author": "Joel H. Nitta [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4719-7472>),\nShawn W. Laffan [ctb, dtc],\nBrent D. Mishler [ctb, dtc],\nWataru Iwasaki [ctb] (ORCID: <https://orcid.org/0000-0002-9169-9245>),\nKlaus Schliep [rev] (ORCID: <https://orcid.org/0000-0003-2941-0161>)",
  "Maintainer": "Joel H. Nitta <joelnitta@gmail.com>",
  "MD5sum": "21e7d461efd633f959bbea40e0c3fa56",
  "_user": "ropensci",
  "_type": "src",
  "_file": "canaper_1.0.1.9000.tar.gz",
  "_fileid": "94b40436adbac51055398f88032e47b0d2c0a370e121c5efd106b5d8fffb81f1",
  "_filesize": 848972,
  "_sha256": "94b40436adbac51055398f88032e47b0d2c0a370e121c5efd106b5d8fffb81f1",
  "_created": "2026-04-17T09:05:23.000Z",
  "_published": "2026-04-17T09:14:41.689Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 71796366372,
      "time": 222,
      "config": "linux-devel-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6492381260"
    },
    {
      "job": 71796366360,
      "time": 210,
      "config": "linux-release-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6492377888"
    },
    {
      "job": 71796366357,
      "time": 167,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6492461813"
    },
    {
      "job": 71796366344,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6492452925"
    },
    {
      "job": 71795734273,
      "time": 219,
      "config": "pkgdown",
      "r": "4.5.2",
      "check": "OK",
      "artifact": "6492299573"
    },
    {
      "job": 71795734301,
      "time": 271,
      "config": "source",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6492314907"
    },
    {
      "job": 71796366335,
      "time": 154,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "OK",
      "artifact": "6492361336"
    },
    {
      "job": 71796366330,
      "time": 197,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6492374030"
    },
    {
      "job": 71796366365,
      "time": 245,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6492387615"
    },
    {
      "job": 71796366323,
      "time": 143,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6492358217"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ropensci/canaper",
  "_commit": {
    "id": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
    "author": "Joel Nitta <joelnitta@gmail.com>",
    "committer": "Joel Nitta <joelnitta@gmail.com>",
    "message": "Bump to dev version\n",
    "time": 1683437085
  },
  "_maintainer": {
    "name": "Joel H. Nitta",
    "email": "joelnitta@gmail.com",
    "login": "joelnitta",
    "mastodon": "@joelnitta@fosstodon.org",
    "bluesky": "@joelnitta.com",
    "orcid": "0000-0003-4719-7472",
    "uuid": 13459362
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "assertr",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "phyloregion",
      "role": "Imports"
    },
    {
      "package": "progressr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    },
    {
      "package": "tictoc",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "picante",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    },
    {
      "package": "fs",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "colorBlindness",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "biodiversity",
    "canape"
  ],
  "_stars": 7,
  "_contributors": [
    {
      "user": "joelnitta",
      "count": 291,
      "uuid": 13459362
    },
    {
      "user": "hadley",
      "count": 1,
      "uuid": 4196
    }
  ],
  "_userbio": {
    "uuid": 1200269,
    "type": "organization",
    "name": "rOpenSci",
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 324,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/canaper"
  },
  "_devurl": "https://github.com/ropensci/canaper",
  "_pkgdown": "https://docs.ropensci.org/canaper",
  "_searchresults": 39,
  "_metadata": {
    "review": {
      "id": 475,
      "status": "reviewed",
      "version": "0.0.1",
      "organization": "rOpenSci Software Review",
      "url": "https://github.com/ropensci/software-review/issues/475"
    },
    "ropensci_category": "stat"
  },
  "_rbuild": "4.5.3",
  "_assets": [
    "extra/canaper.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ropensci/canaper",
  "_realowner": "ropensci",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-10-04"
    },
    {
      "version": "1.0.1",
      "date": "2023-05-05"
    }
  ],
  "_exports": [
    "cpr_classify_endem",
    "cpr_classify_signif",
    "cpr_iter_sim",
    "cpr_make_pal",
    "cpr_rand_comm",
    "cpr_rand_test"
  ],
  "_datasets": [
    {
      "name": "acacia",
      "title": "_Acacia_ example data",
      "object": "acacia",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "biod_example",
      "title": "Biodiverse example data",
      "object": "biod_example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "biod_results",
      "title": "Output from Biodiverse",
      "object": "biod_results",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "site",
        "pd_biodiv",
        "pd_alt_biodiv",
        "rpd_biodiv",
        "pe_biodiv",
        "pe_alt_biodiv",
        "rpe_biodiv"
      ],
      "rows": 127,
      "table": true,
      "tojson": true
    },
    {
      "name": "cpr_endem_cols",
      "title": "CVD-friendly color palette for plotting results of CANAPE",
      "object": "cpr_endem_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cpr_endem_cols_2",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 2",
      "object": "cpr_endem_cols_2",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cpr_endem_cols_3",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 3",
      "object": "cpr_endem_cols_3",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cpr_endem_cols_4",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 4",
      "object": "cpr_endem_cols_4",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cpr_signif_cols",
      "title": "CVD-friendly color palette for plotting results of randomization test",
      "object": "cpr_signif_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cpr_signif_cols_2",
      "title": "CVD-friendly color palette for plotting results of randomization test, version 2",
      "object": "cpr_signif_cols_2",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mishler_endem_cols",
      "title": "Original color palette for plotting results of CANAPE",
      "object": "mishler_endem_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mishler_signif_cols",
      "title": "Original color palette for plotting results of CANAPE",
      "object": "mishler_signif_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "phylocom",
      "title": "Phylocom example data",
      "object": "phylocom",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "acacia",
      "title": "_Acacia_ example data",
      "topics": [
        "acacia"
      ]
    },
    {
      "page": "biod_example",
      "title": "Biodiverse example data",
      "topics": [
        "biod_example"
      ]
    },
    {
      "page": "biod_results",
      "title": "Output from Biodiverse",
      "topics": [
        "biod_results"
      ]
    },
    {
      "page": "cpr_classify_endem",
      "title": "Classify phylogenetic endemism",
      "topics": [
        "cpr_classify_endem"
      ]
    },
    {
      "page": "cpr_classify_signif",
      "title": "Classify statistical significance",
      "topics": [
        "cpr_classify_signif"
      ]
    },
    {
      "page": "cpr_endem_cols",
      "title": "CVD-friendly color palette for plotting results of CANAPE",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_endem_cols"
      ]
    },
    {
      "page": "cpr_endem_cols_2",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 2",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_endem_cols_2"
      ]
    },
    {
      "page": "cpr_endem_cols_3",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 3",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_endem_cols_3"
      ]
    },
    {
      "page": "cpr_endem_cols_4",
      "title": "CVD-friendly color palette for plotting results of CANAPE, version 4",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_endem_cols_4"
      ]
    },
    {
      "page": "cpr_iter_sim",
      "title": "Simulate the number of iterations needed to generate a random community that is sufficiently different from the original community",
      "topics": [
        "cpr_iter_sim"
      ]
    },
    {
      "page": "cpr_make_pal",
      "title": "Make a palette of colors for plotting CANAPE results",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_make_pal"
      ]
    },
    {
      "page": "cpr_rand_comm",
      "title": "Randomize a single community matrix",
      "topics": [
        "cpr_rand_comm"
      ]
    },
    {
      "page": "cpr_rand_test",
      "title": "Run a randomization analysis for one or more biodiversity metrics",
      "topics": [
        "cpr_rand_test"
      ]
    },
    {
      "page": "cpr_signif_cols",
      "title": "CVD-friendly color palette for plotting results of randomization test",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_signif_cols"
      ]
    },
    {
      "page": "cpr_signif_cols_2",
      "title": "CVD-friendly color palette for plotting results of randomization test, version 2",
      "concept": [
        "colors"
      ],
      "topics": [
        "cpr_signif_cols_2"
      ]
    },
    {
      "page": "mishler_endem_cols",
      "title": "Original color palette for plotting results of CANAPE",
      "concept": [
        "colors"
      ],
      "topics": [
        "mishler_endem_cols"
      ]
    },
    {
      "page": "mishler_signif_cols",
      "title": "Original color palette for plotting results of CANAPE",
      "concept": [
        "colors"
      ],
      "topics": [
        "mishler_signif_cols"
      ]
    },
    {
      "page": "phylocom",
      "title": "Phylocom example data",
      "topics": [
        "phylocom"
      ]
    }
  ],
  "_pkglogo": "https://github.com/ropensci/canaper/raw/main/man/figures/logo.png",
  "_readme": "https://github.com/ropensci/canaper/raw/main/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "assertr",
    "assertthat",
    "betapart",
    "class",
    "classInt",
    "cli",
    "cluster",
    "clustMixType",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "DBI",
    "digest",
    "doSNOW",
    "dplyr",
    "e1071",
    "fastmatch",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "geometry",
    "globals",
    "glue",
    "igraph",
    "iterators",
    "itertools",
    "KernSmooth",
    "lattice",
    "lifecycle",
    "linprog",
    "listenv",
    "lpSolve",
    "magic",
    "magrittr",
    "maptpx",
    "MASS",
    "Matrix",
    "mgcv",
    "minpack.lm",
    "nlme",
    "parallelly",
    "permute",
    "phangorn",
    "phyloregion",
    "picante",
    "pillar",
    "pkgconfig",
    "predicts",
    "progressr",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "rcdd",
    "RColorBrewer",
    "Rcpp",
    "RcppProgress",
    "rlang",
    "s2",
    "sf",
    "slam",
    "smoothr",
    "snow",
    "terra",
    "tibble",
    "tidyselect",
    "units",
    "utf8",
    "vctrs",
    "vegan",
    "withr",
    "wk"
  ],
  "_vignettes": [
    {
      "source": "canape.Rmd",
      "filename": "canape.html",
      "title": "CANAPE example",
      "author": "Joel H. Nitta",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Dataset",
        "Randomization test",
        "Classify endemism",
        "Classify significance",
        "Visualize results",
        "References"
      ],
      "created": "2021-06-27 06:44:44",
      "modified": "2023-04-05 20:28:52",
      "commits": 22
    },
    {
      "source": "how-many-rand.Rmd",
      "filename": "how-many-rand.html",
      "title": "How many randomizations?",
      "author": "Joel H. Nitta",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A word about randomization algorithms",
        "Replicates vs. iterations",
        "Effect of n_iterations",
        "Effect of n_reps",
        "Conclusion",
        "References"
      ],
      "created": "2021-10-18 09:28:41",
      "modified": "2023-04-05 20:28:52",
      "commits": 21
    },
    {
      "source": "parallel.Rmd",
      "filename": "parallel.html",
      "title": "Parallel computing",
      "author": "Joel H. Nitta",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How to parallelize",
        "Sequential mode",
        "Parallel mode",
        "When to parallelize?",
        "Progress bars",
        "Conclusion"
      ],
      "created": "2021-10-20 04:52:36",
      "modified": "2023-04-05 20:28:52",
      "commits": 15
    }
  ],
  "_score": 5.612253906096437,
  "_indexed": true,
  "_nocasepkg": "canaper",
  "_universes": [
    "ropensci",
    "joelnitta"
  ],
  "_binaries": [
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:08:15.000Z",
      "distro": "noble",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "748e3697c89ebd89bc7e9ce060e2f8456bef8ad5879d9172ae18dcbe6d09e671",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:13:24.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "4f167ce5d92e7237225b6709e07d97d8d4ba05947c1a35f6ed893bae6b392b24",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:12:44.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "32ba76cbffc56de1de137f2eaa0d5af3f037c53316215a758f27826e10dd377f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.5.1",
      "os": "wasm",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:08:19.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "494dc79f8f8e7177b97039dbf4b2be98e104b106f6735daf5aac337c1cf6e35f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:07:31.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "9bbc528751760fdaa8bbc32c3cff11c77e1831282ddf79a80d2298d2f1c5ca53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:08:27.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "a1f8836a427ba8291042cf399cdcdc6e6ea51f818f6e78e7ec21ef68c9f20791",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1.9000",
      "date": "2026-04-17T09:06:47.000Z",
      "commit": "ea3c4cb9f39c037a66359efb046a712a64da0d80",
      "fileid": "32c21bdfccb327cfc9fbc865eb70a97e0c9e69a90daf76986b7348f91d81ffb6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24556923794"
    }
  ]
}